This is a question I get asked everyday day in my Podiatry clinic, and unfortunately the answer is a tricky one.
Yes, we humans are supposed to be barefoot. But barefoot on natural surfaces such as grass, sand and dirt. It's when we introduce the unforgiving man-made surfaces that we get into trouble. Our bodies are not designed to walk barefoot all day on hard surfaces such as timber, tiles, concrete, bitumen etc. – and let's face it in our modern world this is pretty much what we walk on all day long.
Most people without any foot pain should be able to cope with small amounts of walking barefoot at home on hard man-made surfaces (for example half hour in the morning before going to work and one hour in evening after work). Problems will often occur, and occur quite quickly, when someone is on holidays for a few weeks and sees more time barefoot at home, or when women go on maternity leave, or when people retire. Even a person with the most 'mechanically correct' foot post is likely to develop symptoms from spending long periods of barefoot on hard surfaces. The symptoms may not needlessly show up in your feet either, quite often leg strength, sore knees and sore lower back are often signs or poor shock absorption.
Having said this, spending some barefoot time outside on natural surfaces, or 'earthing', poses many health benefits. Barefoot will help to strengthen your toes, foot and lower leg muscles and also improve your proprioception, awareness and balance. I put this theory to test while traveling through rural Africa for 6 weeks: I wore a pair of tired flip-flops (almost barefoot) for the whole 6 weeks and did a tremendous amount of walking on predominately natural surfaces and suffering no foot or lower leg pain or fatigue. If I did the same thing at home in Australia, with our expanse of man-made surfaces, I'm certain I would have very tired achey feet and legs at the end of my trip.
There is also research out there that suggests 'earthing' improvements things like energy levels, sleep patterns, blood pressure, stress levels and more.
So my suggestion as a Podiatrist who deals with foot pain all day long: limit your barefoot time on hard, man-made surfaces (instead wear cushioned footwear that does not restrict your toes) but make an effort to increase your barefoot time on natural, 'earthy' surfaces.